Escherichia coli is a widespread commensal of the lower intestinal tract of humans and other vertebrates that occasionally causes intestinal and extra-intestinal diseases (Donnenberg 2002). E. coli is used as a probiotic but the currently used probiotic strains, Nissle O6 strain (Mutaflor®) isolated in 1917 from the faeces of a healthy soldier (Sun et al., 2005) and the A0 34/36 O83 strain isolated from porcine faeces (Hejnova, et al., 2005), are highly virulent in a mouse model of extra-intestinal virulence (Johnson et al., 2006).
E. coli colonizes a wide variety of hosts with very diverse gut morphologies and digestive physiologies. E. coli also exhibits quite substantial genetic structure, with most commensal isolates belonging to one of four genetic groups (A, B1, D and B2) (Herzer et al., 1990). The great majority of E. coli strains belonging to genetic group B2 are highly virulent in a mouse model (Johnson et al., 2006).
Epidemiological studies have only demonstrated weak associations between host species and the prevalence of strains of the four phylogenetic groups (Gordon and Cowling 2003; Escobar-Páramo et al., 2006). Although the frequency of the four genetic groups varies to some degree with the diet or body mass of the host from which it was isolated, other factors such as climate, the year of sampling, or the domestication status of the animals sampled (wild versus domesticated) also shape the global genetic structure of E. coli. To date, no strong association between a particular clone and a given host species has been found, except perhaps for a hly B1 clone that appears to be restricted to animals (Gordon and Cowling 2003; Escobar-Páramo et al., 2004b; Escobar-Páramo et al., 2006).
E. coli has been used for many years to assess water quality and to determine the source of any faecal pollution that might occur in a water body (Scott et al., 2002). However, the use of E. coli in these efforts has been hampered by the apparent lack of any extensive host-specificity in E. coli (Gordon, 2001) and by the ability of many E. coli strains to undergo significant cell division in the external environment (Barnes and Gordon, 2004; Power et al., 2005). The usefulness of the microbial indicators as tool risk assessment can be significantly enhanced by the identification of a human specific clone.